rs1801260

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004898(CLOCK):c.*213T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152032 control chromosomes in the gnomAD Genomes database, including 4955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 4955 hom., cov: 32)

Consequence

CLOCK
NM_004898 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.802

Links

CLOCK (HGNC:2082):

TMEM165 (HGNC:30760):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BA1

GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLOCK	NM_004898.4 linkuse as main transcript	c.*213T>C		3_prime_UTR_variant	23/23	ENST00000513440.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLOCK	ENST00000513440.6 linkuse as main transcript	c.*213T>C		3_prime_UTR_variant	23/23	1	NM_004898.4	P1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37470

AN:

152032

Hom.:

4955

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.0993

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.356

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.246

GnomAD4 exome

AF:

0.272

AC:

118169

AN:

435170

Hom.:

16931

AF XY:

0.278

AC XY:

63693

AN XY:

229406

show subpopulations

Gnomad4 AFR exome

AF:

0.179

Gnomad4 AMR exome

AF:

0.218

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.130

Gnomad4 SAS exome

AF:

0.359

Gnomad4 FIN exome

AF:

0.339

Gnomad4 NFE exome

AF:

0.276

Gnomad4 OTH exome

AF:

0.260

Alfa

AF:

0.268

Hom.:

9691

Bravo

AF:

0.226

Asia WGS

AF:

0.261

AC:

908

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

Cadd

Benign

9.2

Dann

Benign

0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over